BME100 f2015:Group4 1030amL6

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BME 100 Fall 2015 Home
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Name: Gabrielle MillsRole(s)
Name: Gabrielle Mills
Name: Christa DeckmanRole(s)
Name: Christa Deckman
Name: Neil RastogiRole(s)
Name: Neil Rastogi
Name: Ngan NguyenRole(s)
Name: Ngan Nguyen
Name: Evan HiggsRole(s)
Name: Evan Higgs
Name: Dylan BunchRole(s)
Name: Dylan Bunch


Bayesian Statistics

Overview of the Original Diagnosis System

In this procedure, thirty-four patients were tested for a disease-associated SNP with seventeen groups analyzed the DNA of two patients each. Each group contained six students. Several procedures were followed to inhibit the acquisition of error within the results. First of all, three samples were taken from each patient to ensure quality results and a lack of contamination affecting them. Secondly, one sample for both a positive and negative control were taken for comparison purposes in the analysis portion of the laboratory procedure. Furthermore, ImageJ was calibrated to eliminate error in the measuring of area and RAWINTDEN of the drops. Lastly, each sample and control had three drop images taken to hinder error in the fluorescence portion of the experiment. For the thirty-four patients, only two patients yielded inconclusive results. Additionally, for two patients there was blank data entered. For the other patients, thirteen got a positive conclusion and seventeen received a negative conclusion. The only problem encountered in the proceeding of this experiment was slightly blurred photos for a good amount of the samples. This led to inaccurate results on the ImageJ measurements.

What Bayes Statistics Imply about This Diagnostic Approach

There is about a 75% chance that the PCR replication of patient's DNA will receive a positive as a final test conclusion, given that he or she has a positive on the PCR reaction. Furthermore, there is about a 90% probability that a patient's conclusion in a PCR replication will be negative, given that he or she in the PCR reaction was negative.

For calculation three, there is around a 25% chance, given that a patient tested positive in the final conclusion, that he or she will get this disease. Additionally, there is a very good chance that the patient will not succumb to the disease, given that he or she got a negative test conclusion.

One possible source of error is the shaking of the camera during the fluorescence activity. This would blur the light in the picture, therefore increasing the measured area of the drop. A second source is the contamination of the PCR samples during the first half of the laboratory experiment, which could distort the samples to either positive, negative or inconclusive results. Finally, a third source of experimental error is the contamination of the positive and negative samples. When comparing the samples to these values, the group may come to the wrong conclusion due to an inaccurate positive and negative value for the controls.

Intro to Computer-Aided Design

The TinkerCad online tool allows amateur, or advanced, designers to piece together new or previously-made pieces into a device. With great maneuverability, the tool was very easy to use to assemble the original and changed versions of the PCR machine. During this lab, this online tool allowed researchers to use pre-made parts to create the Open PCR machine in TinkerCAD and then make the desired changes to it. Compared to Solidworks, the TinkerCad software is very easy to learn and to use. This online program provided valuable tutorials, unlike that of SolidWorks. At the same time, Solidworks has more tools for designing intricate pieces, although they have to be assembled in a completely different document; in contrast, designs can be assembled on the same document in TinkerCAD. Overall, the TinkerCAD software is superior to Solidworks within the range of tools that TinkerCAD offers.

Our Design




In our NRDS device, we made changes in the lid of the Open PCR machine in order to increase ease of use. Our design resembles that of the Open PCR machine in most aspects, although we changed the extruding lid to one that is nested within the PCR device. Other than this, our device looks like the Open PCR machine: cubic, contained, electronic, and convenient. We chose this design because we had a difficult time with the lid on the Open PCR machine, and therefore acknowledge the need for increased ease in starting the PCR.

Feature 1: Consumables

Seeing as our NRDS device appears and works like the Open PCR machine, the same tube sizes will work within our device. The consumables included in our device include pipette tips, a pipettor hanger, PCR mix tubes (empty), PCR mix tubes (including PCR mix), and DNA sample tubes. We consider these components to be the most important in the PCR process.

The NRDS Consumables include:

  • Pipette Tips
  • Pipettor hanger
  • PCR Mix Tubes (Empty)
  • PCR Mix Tubes (including mix)
  • DNA Samples Tubes

Feature 2: Hardware - PCR Machine & Fluorimeter

The Open PCR machine and fluorimeter will be integrated into our system like they were in the lab. After amplifying the DNA in the PCR machine, the fluorimeter will be used to identify subjects testing positive and negative for diseases, when compared to positive and negative controls. The only change to this system will be nesting the lid of the PCR machine in the device itself and creating a new phone clip for androids and iPhones that allows for adjustment when using the fluorimeter.

Two issues arose in the progression of the PCR and fluorimeter labs. The first was present in closing the lid to the PCR machine, and the second consisted of propping an android phone up in the fluorimeter step. Therefore, our group chose to change these two aspects: the lid will now be integrated into the PCR machine so that it does not project outwards, and a stronger and more adjustable clip will be included with the fluorimeter material.

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